The PNW RCE Proteomics, Metabolomics, and Lipidomics (PML) Core provides the resources required for the parallel application of proteomic, metabolomic, and lipidomic analyses to diverse sample sets provide by the RCE collaborators. The integration of data generated by these PML Core approaches with the genomic analyses performed by individual Projects and sub-projects (Project 3 (P01) Dr. Michael Katze, Project 4 (P01) Dr. Michael Gale, and Project 5 (R01) Dr. Fred Heffron), creates a unique opportunity to model disease-related pathways (see Biostatistics and Bioinformatics Core) associated with infection by severe acute respiratory syndrome (SARS) virus, flu virus, Ebola virus, West Nile virus (WNV), Dengue virus (DENV), and Francisella novidica. The PML Core will leverage ongoing technical advances in proteomics (including phosphoproteomics), metabolomics, lipidomics, and informatics resources available at PNNL to generate unique suites of systems biology data by performing high throughput, sensitive, and reproducible protein, metabolite, and lipid abundance measurements on comparative and longitudinal samples for iterative cycles of computational modeling and experimental validation. The PML Core provides both resources and support through multiple stages of proteomics, metabolomics, and lipidomics data acquisition, from construction/augmentation of reference accurate mass and time tag (AMT) tag databases through comparative quantitative analyses. Peptide and lipid coverage in AMT tag databases will be enhanced by advanced liquid chromatography separation methods pioneered at PNNL to reduce sample complexity. In the RCE the PML Core will leverage established and ongoing technological advancements at PNNL accomplished under other support in order to perform the large-scale measurements demanded by the Center collaborations.